FMO DATABASE

FMODB ID: 9GVN2

Calculation Name: 3MJK-F-Xray372

Preferred Name: Platelet-derived growth factor subunit A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3MJK

Chain ID: F

ChEMBL ID: CHEMBL3137294

UniProt ID: P04085

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-896706.053446
FMO2-HF: Nuclear repulsion	845655.89303
FMO2-HF: Total energy	-51050.160416
FMO2-MP2: Total energy	-51194.931191

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(F:23:ALA)

Summations of interaction energy for fragment #1(F:23:ALA)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
1.146	2.649	-0.025	-0.693	-0.785	-0.001

Interaction energy analysis for fragmet #1(F:23:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.027

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	F	25	ILE	0	-0.015	-0.005	3.800	1.308	2.811	-0.025	-0.693	-0.785	-0.001
4	F	26	PRO	0	0.041	0.014	6.666	-0.218	-0.218	0.000	0.000	0.000	0.000
5	F	27	ARG	1	0.998	0.983	8.844	-0.435	-0.435	0.000	0.000	0.000	0.000
6	F	28	GLU	-1	-0.845	-0.915	11.860	0.570	0.570	0.000	0.000	0.000	0.000
7	F	29	VAL	0	0.012	0.013	10.676	-0.089	-0.089	0.000	0.000	0.000	0.000
8	F	30	ILE	0	0.029	0.011	9.879	-0.087	-0.087	0.000	0.000	0.000	0.000
9	F	31	GLU	-1	-0.831	-0.904	13.599	0.111	0.111	0.000	0.000	0.000	0.000
10	F	32	ARG	1	0.773	0.859	14.750	-0.366	-0.366	0.000	0.000	0.000	0.000
11	F	33	LEU	0	0.004	0.007	13.095	-0.026	-0.026	0.000	0.000	0.000	0.000
12	F	34	ALA	0	-0.047	-0.011	17.152	-0.027	-0.027	0.000	0.000	0.000	0.000
13	F	35	ARG	1	0.783	0.889	18.784	-0.164	-0.164	0.000	0.000	0.000	0.000
14	F	36	SER	0	0.004	-0.007	20.033	0.014	0.014	0.000	0.000	0.000	0.000
15	F	37	GLN	0	-0.053	-0.023	22.128	-0.017	-0.017	0.000	0.000	0.000	0.000
16	F	38	ILE	0	0.017	0.004	17.926	0.010	0.010	0.000	0.000	0.000	0.000
17	F	39	HIS	0	-0.066	-0.045	22.203	-0.017	-0.017	0.000	0.000	0.000	0.000
18	F	40	SER	0	-0.012	0.000	22.838	-0.005	-0.005	0.000	0.000	0.000	0.000
19	F	41	ILE	0	0.052	0.019	17.683	0.009	0.009	0.000	0.000	0.000	0.000
20	F	42	ARG	1	0.958	0.988	19.272	-0.014	-0.014	0.000	0.000	0.000	0.000
21	F	43	ASP	-1	-0.836	-0.919	21.191	0.076	0.076	0.000	0.000	0.000	0.000
22	F	44	LEU	0	0.024	0.009	14.699	0.016	0.016	0.000	0.000	0.000	0.000
23	F	45	GLN	0	-0.062	-0.043	16.019	0.023	0.023	0.000	0.000	0.000	0.000
24	F	46	ARG	1	0.929	0.973	16.934	-0.051	-0.051	0.000	0.000	0.000	0.000
25	F	47	LEU	0	-0.008	0.005	17.402	0.018	0.018	0.000	0.000	0.000	0.000
26	F	48	LEU	0	-0.055	-0.008	11.631	0.040	0.040	0.000	0.000	0.000	0.000
27	F	49	GLU	-1	-0.819	-0.898	12.964	0.388	0.388	0.000	0.000	0.000	0.000
28	F	50	ILE	0	-0.051	-0.025	12.701	-0.016	-0.016	0.000	0.000	0.000	0.000
29	F	87	SER	0	0.001	-0.020	27.496	0.000	0.000	0.000	0.000	0.000	0.000
30	F	88	ILE	0	-0.049	-0.011	24.301	0.000	0.000	0.000	0.000	0.000	0.000
31	F	89	GLU	-1	-0.948	-0.974	26.784	-0.039	-0.039	0.000	0.000	0.000	0.000
32	F	90	GLU	-1	-0.860	-0.924	22.853	-0.018	-0.018	0.000	0.000	0.000	0.000
33	F	91	ALA	0	0.005	-0.001	22.284	0.001	0.001	0.000	0.000	0.000	0.000
34	F	92	VAL	0	0.040	0.017	24.159	0.007	0.007	0.000	0.000	0.000	0.000
35	F	93	PRO	0	0.013	0.012	23.098	-0.009	-0.009	0.000	0.000	0.000	0.000
36	F	94	ALA	0	0.013	0.007	24.892	0.008	0.008	0.000	0.000	0.000	0.000
37	F	95	VAL	0	0.024	-0.004	26.402	-0.003	-0.003	0.000	0.000	0.000	0.000
38	F	96	CYS	0	0.006	0.028	24.561	0.008	0.008	0.000	0.000	0.000	0.000
39	F	97	LYS	1	0.968	0.973	28.786	0.024	0.024	0.000	0.000	0.000	0.000
40	F	98	THR	0	0.034	0.017	32.552	-0.006	-0.006	0.000	0.000	0.000	0.000
41	F	99	ARG	1	0.795	0.885	29.965	0.038	0.038	0.000	0.000	0.000	0.000
42	F	100	THR	0	-0.055	-0.062	36.570	0.000	0.000	0.000	0.000	0.000	0.000
43	F	101	VAL	0	0.010	0.010	34.762	-0.003	-0.003	0.000	0.000	0.000	0.000
44	F	102	ILE	0	0.011	-0.003	38.060	0.003	0.003	0.000	0.000	0.000	0.000
45	F	103	TYR	0	-0.024	-0.015	39.061	-0.003	-0.003	0.000	0.000	0.000	0.000
46	F	104	GLU	-1	-0.911	-0.966	41.258	-0.043	-0.043	0.000	0.000	0.000	0.000
47	F	105	ILE	0	-0.038	-0.020	43.186	0.000	0.000	0.000	0.000	0.000	0.000
48	F	106	PRO	0	0.037	0.019	43.060	-0.001	-0.001	0.000	0.000	0.000	0.000
49	F	107	ARG	1	0.920	0.958	45.325	0.035	0.035	0.000	0.000	0.000	0.000
50	F	108	SER	0	0.039	-0.002	45.067	0.002	0.002	0.000	0.000	0.000	0.000
51	F	109	GLN	0	0.006	0.001	44.746	0.001	0.001	0.000	0.000	0.000	0.000
52	F	110	VAL	0	-0.037	-0.005	48.454	0.002	0.002	0.000	0.000	0.000	0.000
53	F	111	ASP	-1	-0.766	-0.871	51.663	-0.023	-0.023	0.000	0.000	0.000	0.000
54	F	112	PRO	0	0.005	0.002	49.992	-0.001	-0.001	0.000	0.000	0.000	0.000
55	F	113	THR	0	-0.078	-0.039	51.472	-0.001	-0.001	0.000	0.000	0.000	0.000
56	F	114	SER	0	-0.047	-0.028	54.423	-0.001	-0.001	0.000	0.000	0.000	0.000
57	F	115	ALA	0	0.052	0.015	51.775	-0.001	-0.001	0.000	0.000	0.000	0.000
58	F	116	ASN	0	-0.027	-0.018	53.395	-0.001	-0.001	0.000	0.000	0.000	0.000
59	F	117	PHE	0	-0.051	-0.015	52.070	0.001	0.001	0.000	0.000	0.000	0.000
60	F	118	LEU	0	-0.009	0.003	52.370	-0.002	-0.002	0.000	0.000	0.000	0.000
61	F	119	ILE	0	0.027	0.019	48.677	0.001	0.001	0.000	0.000	0.000	0.000
62	F	120	TRP	0	0.020	0.027	51.874	-0.001	-0.001	0.000	0.000	0.000	0.000
63	F	121	PRO	0	0.071	0.023	49.960	0.001	0.001	0.000	0.000	0.000	0.000
64	F	122	PRO	0	0.010	0.000	47.578	0.000	0.000	0.000	0.000	0.000	0.000
65	F	123	CYS	0	-0.022	-0.010	44.040	-0.002	-0.002	0.000	0.000	0.000	0.000
66	F	124	VAL	0	-0.006	0.002	44.784	0.002	0.002	0.000	0.000	0.000	0.000
67	F	125	GLU	-1	-0.801	-0.865	42.674	-0.027	-0.027	0.000	0.000	0.000	0.000
68	F	126	VAL	0	-0.046	-0.015	39.841	0.002	0.002	0.000	0.000	0.000	0.000
69	F	127	LYS	1	0.852	0.934	39.377	0.020	0.020	0.000	0.000	0.000	0.000
70	F	128	ARG	1	0.858	0.917	35.189	0.033	0.033	0.000	0.000	0.000	0.000
71	F	129	CYS	0	-0.048	0.001	31.855	-0.002	-0.002	0.000	0.000	0.000	0.000
72	F	130	THR	0	0.030	0.011	30.349	-0.004	-0.004	0.000	0.000	0.000	0.000
73	F	131	GLY	0	0.028	0.012	27.593	0.006	0.006	0.000	0.000	0.000	0.000
74	F	132	CYS	0	-0.060	-0.036	22.371	-0.010	-0.010	0.000	0.000	0.000	0.000
75	F	133	CYS	0	-0.027	0.018	21.897	0.003	0.003	0.000	0.000	0.000	0.000
76	F	134	ASN	0	-0.015	-0.015	18.399	-0.026	-0.026	0.000	0.000	0.000	0.000
77	F	135	THR	0	0.047	0.044	15.009	-0.029	-0.029	0.000	0.000	0.000	0.000
78	F	136	SER	0	0.037	0.014	16.247	0.006	0.006	0.000	0.000	0.000	0.000
79	F	137	SER	0	-0.049	-0.029	16.369	0.005	0.005	0.000	0.000	0.000	0.000
80	F	138	VAL	0	-0.062	-0.028	18.338	0.018	0.018	0.000	0.000	0.000	0.000
81	F	139	LYS	1	0.937	0.969	21.191	0.054	0.054	0.000	0.000	0.000	0.000
82	F	141	GLN	0	0.019	0.006	27.559	-0.007	-0.007	0.000	0.000	0.000	0.000
83	F	142	PRO	0	0.026	-0.001	30.460	0.005	0.005	0.000	0.000	0.000	0.000
84	F	143	SER	0	-0.031	-0.048	34.238	-0.001	-0.001	0.000	0.000	0.000	0.000
85	F	144	ARG	1	0.811	0.885	35.711	-0.001	-0.001	0.000	0.000	0.000	0.000
86	F	145	VAL	0	0.012	-0.001	38.164	-0.002	-0.002	0.000	0.000	0.000	0.000
87	F	146	HIS	0	-0.012	-0.009	40.694	0.001	0.001	0.000	0.000	0.000	0.000
88	F	147	HIS	0	0.035	0.028	42.161	-0.003	-0.003	0.000	0.000	0.000	0.000
89	F	148	ARG	1	0.882	0.917	46.019	0.020	0.020	0.000	0.000	0.000	0.000
90	F	149	SER	0	-0.018	-0.014	48.796	-0.002	-0.002	0.000	0.000	0.000	0.000
91	F	150	VAL	0	-0.022	-0.002	49.834	0.001	0.001	0.000	0.000	0.000	0.000
92	F	151	LYS	1	0.836	0.898	52.585	0.015	0.015	0.000	0.000	0.000	0.000
93	F	152	VAL	0	0.004	0.014	50.820	0.000	0.000	0.000	0.000	0.000	0.000
94	F	153	ALA	0	0.000	-0.013	54.291	0.001	0.001	0.000	0.000	0.000	0.000
95	F	154	LYS	1	0.782	0.900	55.385	0.022	0.022	0.000	0.000	0.000	0.000
96	F	155	VAL	0	0.012	-0.010	56.641	0.001	0.001	0.000	0.000	0.000	0.000
97	F	156	GLU	-1	-0.767	-0.881	57.653	-0.023	-0.023	0.000	0.000	0.000	0.000
98	F	157	TYR	0	0.044	0.014	60.100	0.001	0.001	0.000	0.000	0.000	0.000
99	F	158	VAL	0	0.032	0.028	62.338	0.000	0.000	0.000	0.000	0.000	0.000
100	F	159	ARG	1	0.938	0.949	64.608	0.018	0.018	0.000	0.000	0.000	0.000
101	F	160	LYS	1	0.984	0.986	65.503	0.020	0.020	0.000	0.000	0.000	0.000
102	F	161	LYS	1	0.985	1.006	66.580	0.016	0.016	0.000	0.000	0.000	0.000
103	F	162	PRO	0	0.007	0.023	63.986	0.000	0.000	0.000	0.000	0.000	0.000
104	F	163	LYS	1	0.925	0.947	63.471	0.017	0.017	0.000	0.000	0.000	0.000
105	F	164	LEU	0	0.002	0.007	60.037	-0.001	-0.001	0.000	0.000	0.000	0.000
106	F	165	LYS	1	0.873	0.931	59.465	0.020	0.020	0.000	0.000	0.000	0.000
107	F	166	GLU	-1	-0.793	-0.878	58.485	-0.017	-0.017	0.000	0.000	0.000	0.000
108	F	167	VAL	0	-0.027	-0.003	54.009	0.000	0.000	0.000	0.000	0.000	0.000
109	F	168	GLN	0	0.020	0.012	53.487	0.000	0.000	0.000	0.000	0.000	0.000
110	F	169	VAL	0	0.020	0.008	48.044	-0.001	-0.001	0.000	0.000	0.000	0.000
111	F	170	ARG	1	0.929	0.960	47.232	0.019	0.019	0.000	0.000	0.000	0.000
112	F	171	LEU	0	-0.010	0.003	44.904	-0.002	-0.002	0.000	0.000	0.000	0.000
113	F	172	GLU	-1	-0.801	-0.878	38.120	-0.030	-0.030	0.000	0.000	0.000	0.000
114	F	173	GLU	-1	-0.778	-0.878	40.927	-0.023	-0.023	0.000	0.000	0.000	0.000
115	F	174	HIS	0	-0.013	-0.020	35.000	0.001	0.001	0.000	0.000	0.000	0.000
116	F	175	LEU	0	-0.030	-0.018	38.958	0.000	0.000	0.000	0.000	0.000	0.000
117	F	176	GLU	-1	-0.802	-0.848	35.769	0.005	0.005	0.000	0.000	0.000	0.000
118	F	178	ALA	0	0.044	0.020	30.247	0.005	0.005	0.000	0.000	0.000	0.000
119	F	180	ALA	0	0.032	0.006	25.861	0.010	0.010	0.000	0.000	0.000	0.000
120	F	181	THR	0	0.016	0.005	23.448	-0.016	-0.016	0.000	0.000	0.000	0.000
121	F	182	THR	0	0.008	-0.013	24.359	0.001	0.001	0.000	0.000	0.000	0.000
122	F	183	SER	0	-0.002	0.018	25.715	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:23:ALA)